It would be fantastic to be able to setup a cron job active scanner that would check all the core files of Joomla periodically. If Joomla had a hash value for files in the core it could run checks on itself. Also using the install XML files of third party extensions it could identify files that are not supposed to be on the server. The scanner could then email the supper admin to report possible breaches of security.

Finally if the scanner could check permissions too it would help the administrator find potential security holes before bad spiders do.

I think Doctrine ORM is the best data persistence model in PHP as it is similar to Hibernate to(an open source Java persistence framework project) as Doctrine is also OSS, so joomla quality will automatically increase as Doctrine will develop itself

When you add an article you have to go and make a menu link, there should be an option to automtically add to menu mod. (all level choices) as you add the article, and option not to if you just want to add arbituary article, 1.0 had this but only one level. That is a core part of content creation

There should be an option in categories' article list module to display them hierarchically. There is an option to nest article categories, creating subcategories. There is an option to list all articles with subcategories.

Create an option that should allow administrators to clean install Joomla i.e. re-install from scratch after clearing all the existing installation. This is mainly needed when experienced any hacking or malware attack on the site.